Screening for Enantioselective Enzymes

Reference work entry
Part of the Handbook of Hydrocarbon and Lipid Microbiology book series (HHLM)

Abstract

A wealth of novel enzyme genes is accessible from natural sources, from genome and metagenome sequencing projects, and from libraries created by directed evolution. However, the identification of novel enzyme activities with a high potential for biotechnological applications still represents a major bottleneck. Here, assays are needed allowing to screen for enzyme activities and enantioselectivities. Hence, we describe several assays carried out on agar plates or in solution which are based on photometry, fluorometry, chromatography, electrophoresis, spectrometry, and spectroscopy.

References

  1. Arnold FH, Georgiou G (2003) Directed evolution library creation: methods and protocols. Humana Press, TotowaCrossRefGoogle Scholar
  2. Babiak P, Reymond JL (2005) A high-throughput, low-volume enzyme assay on solid support. Anal Chem 77:373–377CrossRefPubMedGoogle Scholar
  3. Badalassi F, Wahler D, Klein G, Crotti P, Reymond JL (2000) A versatile periodate-coupled fluorogenic assay for hydrolytic enzymes. Angew Chem Int Ed 39:4067–4070CrossRefGoogle Scholar
  4. Basile F, Ferrer I, Furlong ET, Voorhees KJ (2002) Simultaneous multiple substrate tag detection with ESI-ion trap MS for in vivo bacterial enzyme activity profiling. Anal Chem 74:4290–4293CrossRefPubMedGoogle Scholar
  5. Baumann M, Stürmer R, Bornscheuer UT (2001) A high-throughput-screening method for the identification of active and enantioselective hydrolases. Angew Chem Int Ed 40:4201–4204CrossRefGoogle Scholar
  6. Beisson F, Tiss A, Rivière C, Verger R (2000) Methods for lipase detection and assay: a critical review. Eur J Lipid Sci Technol 102:133–153CrossRefGoogle Scholar
  7. Belder D, Ludwig M, Wang LW, Reetz MT (2006) Enantioselective catalysis and analysis on a chip. Angew Chem Int Ed 45:2463–2466CrossRefGoogle Scholar
  8. Beloqui A, de Maria PD, Golyshin PN, Ferrer M (2008) Recent trends in industrial microbiology. Curr Opin Microbiol 11:240–248CrossRefPubMedGoogle Scholar
  9. Birner-Grünberger R, Schmidinger H, Loidl A, Scholze H, Hermetter A (2006) Fluorescent probes for lipolytic enzymes. In: Reymond JL (ed) Enzyme assays: high-throughput screening, genetic selection and fingerprinting. Wiley-VCH, Weinheim, pp 241–269Google Scholar
  10. Blanco M, Valverde I (2003) Choice of chiral selector for enantioseparation by capillary electrophoresis trends. Anal Chem 22:428–439Google Scholar
  11. Brakmann S, Johnsson K (2002) Directed molecular evolution of proteins: or how to improve enzymes for biocatalysis. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  12. Brakmann S, Schwienhorst A (2004) Evolutionary methods in biotechnology: clever tricks for directed evolution. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  13. Buissière J, Fourcard A, Colobert L (1967) Usage de substrats synthétiques pour l’étude de l’équipement enzymatique de microorganismes. C R Acad Sci Hebd Seances Acad Sci D 264:415–417PubMedGoogle Scholar
  14. Cedrone F, Niel S, Roca S, Bhatnagar T, Ait-Abdelkader N, Torre C, Krumm H, Maichele A, Reetz MT, Baratti JC (2003) Directed evolution of the epoxide hydrolase from Aspergillus niger. Biocatal Biotransform 21:357–364CrossRefGoogle Scholar
  15. Classen T, Kovacic F, Lauinger B, Pietruszka J, Jaeger KE (2017) Screening for enantioselective lipases. In: McGenity TJ, Timmis KN, Nogales Fernández B (eds) Hydrocarbon and lipid microbiology protocols. Springer, Berlin-Heidelberg, pp 37–69Google Scholar
  16. Dale JA, Mosher HS (1973) Nuclear magnetic resonance enantiomer reagents. Configurational correlations via nuclear magnetic resonance chemical shifts of diastereomeric mandelate, O-methylmandelate, and α-methoxy-α-trifluoromethylphenylacetate (MTPA) esters. J Am Chem Soc 95:512–519CrossRefGoogle Scholar
  17. DeSantis G, Wong K, Farwell B, Chatman K, Zhu Z, Tomlinson G, Huang H, Tan X, Bibbs L, Chen P, Kretz K, Burk MJ (2003) Creation of a productive, highly enantioselective nitrilase through gene site saturation mutagenesis (GSSM). J Am Chem Soc 125:11476–11477CrossRefPubMedGoogle Scholar
  18. Drauz K, Waldmann H (2002) Enzyme catalysis in organic synthesis. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  19. de Laborde de Monpezat T, De Jeso B, Butour J-L, Chavant L, Sabcholle M (1990) A fluorimetric method for measuring lipase activity based on umbelliferyl esters. Lipids 25:661–664CrossRefGoogle Scholar
  20. Elend C, Schmeisser C, Leggewie C, Babiak P, Carballeira JD, Steele HL, Reymond JL, Jaeger KE, Streit WR (2006) Isolation and biochemical characterization of two novel metagenome-derived esterases. Appl Environ Microbiol 72:3637–3645CrossRefPubMedPubMedCentralGoogle Scholar
  21. Evans MA, Morken JP (2002) Isotopically chiral probes for in situ high-throughput asymmetric reaction analysis. J Am Chem Soc 124:9020–9091CrossRefPubMedGoogle Scholar
  22. Ferrer M, Martinez-Abarca F, Golyshin PN (2005) Mining genomes and “metagenomes” for novel catalysts. Curr Opin Biotechnol 16:588–593CrossRefPubMedGoogle Scholar
  23. Fessner WD, Anthonsen T (2009) Modern biocatalysis. Wiley-VCH, WeinheimGoogle Scholar
  24. Funke SA, Eipper A, Reetz MT, Otte N, Thiel W, van Pouderoyen G, Dijkstra BW, Jaeger K-E, Eggert T (2003) Directed evolution of an enantioselective Bacillus subtilis lipase. Biocatal Biotransform 21:67–73CrossRefGoogle Scholar
  25. Goddard JP, Reymond JL (2004) Enzyme activity fingerprinting with substrate cocktails. J Am Chem Soc 126:11116–11117CrossRefPubMedGoogle Scholar
  26. Gosalia DN, Diamond SL (2003) Printing chemical libraries on microarrays for fluid phase nanoliter reactions. Proc Natl Acad Sci U S A 100:8721–8726CrossRefPubMedPubMedCentralGoogle Scholar
  27. Goujard L, Villeneuve P, Barea B, Lecomte J, Pina M, Claude S, Le Petit J, Ferré J (2009) A spectrophotometric transesterification-based assay for lipases in organic solvents. Anal Biochem 385:161–167CrossRefPubMedGoogle Scholar
  28. Grognux J, Reymond JL (2004) Classifying enzymes from selectivity fingerprints. Chembiochem 5:826–831CrossRefPubMedGoogle Scholar
  29. Grognux J, Reymond JL (2006) A red-fluorescent substrate microarray for lipase fingerprinting. Mol BioSyst 2:492–498CrossRefPubMedGoogle Scholar
  30. Henke E, Bornscheuer UT (1999) Directed evolution of an esterase from Pseudomonas fluorescens. Random mutagenesis by error-prone PCR or a mutator strain and identification of mutants showing enhanced enantioselectivity by a resorufin-based fluorescence assay. Biol Chem 380:1029–1033CrossRefPubMedGoogle Scholar
  31. Horeau A, Nouaille A (1990) Micromethode de determination de la configuration des alcools secondaires par dedoublement cinetique. Emploi de la spectrographie de masse. Tetrahedron Lett 31:2707–2710CrossRefGoogle Scholar
  32. Humble MW, King A, Phillips I (1977) API ZYM: a simple rapid system for the detection of bacterial enzymes. J Clin Pathol 30:275–277CrossRefPubMedPubMedCentralGoogle Scholar
  33. Illanes A (2008) Enzyme biocatalysis: principles and applications. Springer, DordrechtCrossRefGoogle Scholar
  34. Jaeger KE, Eggert T (2002) Lipases for biotechnology. Curr Opin Biotechnol 13:390–397CrossRefPubMedGoogle Scholar
  35. Janes LE, Kazlauskas RJ (1997) Quick E A fast spectrophotometric method to measure the enantioselectivity of hydrolases. J Org Chem 62:4560–4561CrossRefGoogle Scholar
  36. Janes LE, Löwendahl AC, Kazlauskas RJ (1998) Quantitative screening of hydrolase libraries using pH indicators: identifying active and enantioselective hydrolases. Chem Eur J 4:2324–2331CrossRefGoogle Scholar
  37. Klein G, Reymond JL (1999) Enantioselective fluorogenic assay of acetate hydrolysis for detecting lipase catalytic antibodies. Helv Chim Acta 82:400–407CrossRefGoogle Scholar
  38. Konarzycka-Bessler M, Bornscheuer UT (2003) A high-throughput-screening method for determining the synthetic activity of hydrolases. Angew Chem Int Ed 42:1418–1420CrossRefGoogle Scholar
  39. Kouker G, Jaeger KE (1987) Specific and sensitive plate assay for bacterial lipases. Appl Environ Microbiol 53:211–213PubMedPubMedCentralGoogle Scholar
  40. Lawrence RT, Fryer TF, Reiter B (1967) Rapid method for the quantitative estimation of microbial lipases. Nature 213:1264–1265CrossRefGoogle Scholar
  41. Li Z, Butikofer L, Witholt B (2004) High-throughput measurement of the enantiomeric excess of chiral alcohols by using two enzymes. Angew Chem Int Ed 43:1698–1702CrossRefGoogle Scholar
  42. Liebeton K, Zonta A, Schimossek K, Nardini M, Lang D, Dijkstra BW, Reetz MT, Jaeger KE (2000) Directed evolution of an enantioselective lipase. Chem Biol 7:709–718CrossRefPubMedGoogle Scholar
  43. Liebl W, Angelov A, Juergensen J, Chow J, Loeschcke A, Drepper T, Classen T, Pietruszka J, Ehrenreich A, Streit WR, Jaeger KE (2014) Alternative hosts for functional (meta)genome analysis. Appl Micriobiol Biotechnol 98:8099–8109CrossRefGoogle Scholar
  44. Liese A, Seelbach K, Wandrey C (2006) Industrial biotransformations. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  45. Liu AMF, Somers NA, Kazlauskas RJ, Brush TS, Zocher F, Enzelberger MM, Bornscheuer UT, Horsman GP, Mezzetti A, Schmidt-Dannert C, Schmid RD (2001) Mapping the substrate selectivity of new hydrolases using colorimetric screening: lipases from Bacillus thermocatenulatus and Ophiostoma piliferum, esterases from Pseudomonas fluorescens and Streptomyces diastatochromogenes. Tetrahedron Asymmetry 12:545–556CrossRefGoogle Scholar
  46. Morís-Varas F, Shah A, Aikens J, Nadkarni NP, Rozzell JD, Demirjian DC (1999) Visualization of enzyme-catalyzed reactions using pH indicators: rapid screening of hydrolase libraries and estimation of the enantioselectivity. Bioorg Med Chem 7:2183–2188CrossRefPubMedGoogle Scholar
  47. Nagahori N, Nishimura S (2006) Direct and efficient monitoring of glycosyltransferase reactions on gold colloidal nanoparticles by using mass spectrometry. Chemistry 12:6478–6485CrossRefPubMedGoogle Scholar
  48. Paegel BM, Blazej RG, Mathies RA (2005) Microfabricated DNA sequencing devices. In: Nunnally BK (ed) Analytical techniques in DNA sequencing. Taylor & Francis, Boca Raton, pp 61–83Google Scholar
  49. Polaina J, MacCabe AP (2008) Industrial enzymes: structure, function and applications. Springer, New YorkGoogle Scholar
  50. Reetz MT (2004) Controlling the enantioselectivity of enzymes by directed evolution: practical and theoretical ramifications. Proc Natl Acad Sci U S A 101:5716–5722CrossRefPubMedPubMedCentralGoogle Scholar
  51. Reetz MT (2006) Directed evolution of enantioselective enzymes as catalysts for organic synthesis. In: Gates BC, Knozinger H (eds) Advances in catalysis, vol 49. Elsevier, San Diego, pp 2–69Google Scholar
  52. Reetz MT, Zonta A, Schimossek K, Liebeton K, Jaeger KE (1997) Creation of enantioselective biocatalysts for organic chemistry by in vitro evolution. Angew Chem Int Ed Eng 36:2830–2832CrossRefGoogle Scholar
  53. Reetz MT, Becker MH, Klein HW, Stöckigt D (1999) A method for high-throughput screening of enantioselective catalysts. Angew Chem Int Ed 38:1758–1761CrossRefGoogle Scholar
  54. Reetz MT, Kühling KM, Deege A, Hinrichs H, Belder D (2000) Super-high-throughput screening of enantioselective catalysts by using capillary array electrophoresis. Angew Chem Int Ed Eng 39:3891–3893CrossRefGoogle Scholar
  55. Reetz MT, Kühling KM, Wilensek S, Husmann H, Häusig UW, Hermes M (2001) A GC-based method for high-throughput screening of enantioselective catalysts. Catal Today 67:389–396CrossRefGoogle Scholar
  56. Reetz MT, Eipper A, Tielmann P, Mynott R (2002) A practical NMR-based high-throughput assay for screening enantioselective catalysts and biocatalysts. Adv Synth Catal 344:1008–1016CrossRefGoogle Scholar
  57. Reetz MT, Brunner B, Schneider T, Schulz F, Clouthier CM, Kayser MM (2004a) Directed evolution as a method to create enantioselective cyclohexanone monooxygenases for catalysis in Baeyer-Villiger reactions. Angew Chem Int Ed 43:4075–4078CrossRefGoogle Scholar
  58. Reetz MT, Daligault F, Brunner B, Hinrichs H, Deege A (2004b) Directed evolution of cyclohexanone monooxygenases: enantioselective biocatalysts for the oxidation of prochiral thioethers. Angew Chem Int Ed 43:4078–4081CrossRefGoogle Scholar
  59. Reetz MT, Tielmann P, Eipper A, Ross A, Schlotterbeck G (2004c) A high-throughput NMR-based ee-assay using chemical shift imaging. Chem Commun 4:1366–1367CrossRefGoogle Scholar
  60. Reetz MT, Torre C, Eipper A, Lohmer R, Hermes M, Brunner B, Maichele A, Bocola M, Arand M, Cronin A, Genzel Y, Archelas A, Furstoss R (2004d) Enhancing the enantioselectivity of an epoxide hydrolase by directed evolution. Org Lett 6:177–180CrossRefPubMedGoogle Scholar
  61. Reymond JL (2006) Enzyme assays: high-throughput screening, genetic selection and fingerprinting. Wiley-VCH, WeinheimGoogle Scholar
  62. Reymond JL (2009) Colorimetric and fluorescense-based screening. In: Lutz S, Bornscheuer UT (eds) Protein engineering handbook, vol 2. Wiley-VCH, Weiheim, pp 669–711Google Scholar
  63. Reymond JL, Babiak P (2007) Screening systems. In: Ulber R, Sell D (eds) White biotechnology, vol 105. Springer, Berlin, pp 31–58CrossRefGoogle Scholar
  64. Reymond JL, Wahler D (2002) Substrate arrays as enzyme fingerprinting tools. Chembiochem 3:701–708CrossRefPubMedGoogle Scholar
  65. Reymond JL, Fluxa VS, Maillard N (2009) Enzyme assays. Chem Commun (Camb) 1:34–46Google Scholar
  66. Rothenberg G (2008) Catalysis: concepts and green applications. Wiley-VCH, WeinheimCrossRefGoogle Scholar
  67. Schmidt M, Bornscheuer UT (2005) High-throughput assays for lipases and esterases. Biomol Eng 22:51–56CrossRefPubMedGoogle Scholar
  68. Schmidt-Dannert C, Arnold FH (1999) Directed evolution of industrial enzymes. Trends Biotechnol 17:135–136CrossRefPubMedGoogle Scholar
  69. Schrader W, Eipper A, Pugh DJ, Reetz MT (2002) Second-generation MS-based high-throughput screening system for enantioselective catalysts and biocatalysts. Can J Chems 80:626–632CrossRefGoogle Scholar
  70. Sheldon RA, Arends I, Hanefeld U (2007) Green chemistry and catalysis. Wiley-VCH, WeiheimCrossRefGoogle Scholar
  71. Sicard R, Goddard JP, Mazel M, Audiffrin C, Fourage L, Ravot G, Wahler D, Lefèvre F, Reymond JL (2005) Multienzyme profiling of thermophilic microorganisms with a substrate cocktail assay. Adv Synth Catal 347:987–996CrossRefGoogle Scholar
  72. Steele HL, Jaeger KE, Daniel R, Streit WR (2009) Advances in recovery of novel biocatalysts from metagenomes. J Mol Microbiol Biotechnol 16:25–37CrossRefPubMedGoogle Scholar
  73. Teng Y, Xu Y (2007) A modified para-nitrophenyl palmitate assay for lipase synthetic activity determination in organic solvent. Anal Biochem 363:297–299CrossRefPubMedGoogle Scholar
  74. Tielmann P, Boese M, Luft M, Reetz MT (2003) A practical high-throughput screening system for enantioselectivity by using FTIR spectroscopy. Chem Eur J 9:3882–3887CrossRefPubMedGoogle Scholar
  75. Trapp O (2008) High-throughput monitoring of interconverting stereoisomers and catalytic reactions. Chim Oggi 26:26–28Google Scholar
  76. Turner NJ (2006) Agar plate-based assays. In: Reymond JL (ed) Enzyme assays: high-throughput screening, genetic selection and fingerprinting. Wiley-VCH, Weinheim, pp 139–161Google Scholar
  77. Vinod Kumar KS, Ramasubhan B, Lakshmi BS, Gautam P (2006) A sensitive assay for lipase using tetra sulfonatophenyl porphyrin. Anal Biochem 356:294–296CrossRefPubMedGoogle Scholar
  78. Wahler D, Badalassi F, Crotti P, Reymond JL (2001) Enzyme fingerprints by fluorogenic and chromogenic substrate arrays. Angew Chem Int Ed 40:4457–4460CrossRefGoogle Scholar
  79. Wahler D, Badalassi F, Crotti P, Reymond JL (2002) Enzyme fingerprints of activity, and stereo- and enantioselectivity from fluorogenic and chromogenic substrate arrays. Chemistry 8:3211–3228CrossRefPubMedGoogle Scholar
  80. Wahler D, Boujard O, Lefèvre F, Reymond JL (2004) Adrenaline profiling of lipases and esterases with 1,2-diol and carbohydrate acetates. Tetrahedron 60:703–710CrossRefGoogle Scholar
  81. Wang P, Wang L, Li C, Wang R, Miao Q, Yang M, Wang Z (2009) Rapid estimation of enantioselectivity in lipase-catalyzed resolution of glycidyl butyrate using pH indicator. Chem Res Chin Univ 22:72–75Google Scholar
  82. Winkler UK, Stuckmann M (1979) Glycogen, hyaluronate, and some other polysaccharides greatly enhance the formation of exolipase by Serratia marcescens. J Bacteriol 138:663–670PubMedPubMedCentralGoogle Scholar
  83. Yang Y, Babiak P, Reymond JL (2006) New monofunctionalized fluorescein derivatives for the efficient high-throughput screening of lipases and esterases in aqueous media. Helv Chim Acta 89:404–415CrossRefGoogle Scholar
  84. Yongzheng Y, Reymond JL (2005) Protease profiling using a fluorescent domino peptide cocktail. Mol BioSyst 1:57–63CrossRefPubMedGoogle Scholar
  85. Zha D, Eipper A, Reetz MT (2003) Assembly of designed oligonucleotides as an efficient method for gene recombination: a new tool in directed evolution. Chembiochem 4:34–39CrossRefPubMedGoogle Scholar

Copyright information

© Springer International Publishing AG, part of Springer Nature 2017

Authors and Affiliations

  1. 1.System SolutionsQiagen GmbHHildenGermany
  2. 2.Institute of Molecular Enzyme TechnologyHeinrich-Heine University Duesseldorf, Research Center JuelichJuelichGermany
  3. 3.Institute of Bioorganic ChemistryHeinrich-Heine University Duesseldorf, Research Center JuelichJuelichGermany

Personalised recommendations